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Janjua, S., Peters, J. L., Weckworth, B., Abbas, F. I., Bahn, Volker, Johansson, O., Rooney, T.P. (2019). Improving our conservation genetic toolkit: ddRAD-seq for SNPs in snow leopards. Conservation Genetic Resource, .
Abstract: Snow leopards (Panthera uncia) are an enigmatic, high-altitude species whose challenging habitat, low population densities
and patchy distribution have presented challenges for scientists studying its biology, population structure, and genetics.
Molecular scatology brings a new hope for conservation efforts by providing valuable insights about snow leopards, including
their distribution, population densities, connectivity, habitat use, and population structure for assigning conservation units.
However, traditional amplification of microsatellites from non-invasive sources of DNA are accompanied by significant
genotyping errors due to low DNA yield and poor quality. These errors can lead to incorrect inferences in the number of
individuals and estimates of genetic diversity. Next generation technologies have revolutionized the depth of information
we can get from a species' genome. Here we used double digest restriction-site associated DNA sequencing (ddRAD-seq),
a well-established technique for studying non-model organisms, to develop a reference sequence library for snow leopards
using blood samples from five Mongolian individuals. Our final data set reveals 4504 loci with a median size range of 221 bp.
We identified 697 SNPs and low nucleotide diversity (0.00032) within these loci. However, the probability that two random
individuals will share identical genotypes is about 10-168. We developed probes for DNA capture using this sequence library
which can now be used for genotyping individuals from scat samples. Genetic data from ddRAD-seq will be invaluable for
conducting population and landscape scale studies that can inform snow leopard conservation strategies.
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Janecka, J.E., Jackson, R., Yuquang, Z., Diqiang, L., Munkhtsog, B., et al. (2008). Population monitoring of snow leopards using noninvasive collection of scat samples: a pilot study (Vol. 11).
Abstract: The endangered snow leopard Panthera uncia occurs in rugged, high-altitude regions of Central Asia. However, information on the status of this felid is limited in many areas. We conducted a pilot study to optimize molecular markers for the analysis of snow leopard scat samples and to examine the feasibility of using noninvasive genetic methods for monitoring this felid. We designed snow leopard-specific primers for seven microsatellite loci that amplified shorter segments and avoided flanking sequences shared with repetitive elements. By redesigning primers we maximized genotyping success and minimized genotyping errors. In addition, we tested a Y chromosome-marker for sex identification and designed a panel of mitochondrial DNA primers for examining genetic diversity of snow leopards using scat samples. We collected scats believed to be from snow leopards in three separate geographic regions including north-western India, central China and southern Mongolia. We observed snow leopard scats in all three sites despite only brief 2-day surveys in each area. There was a high rate of species misidentification in the field with up to 54% of snow leopard scats misidentified as red fox. The high rate of field misidentification suggests sign surveys incorporating scat likely overestimate snow leopard abundance. The highest ratio of snow leopard scats was observed in Ladakh (India) and South Gobi (Mongolia), where four and five snow leopards were detected, respectively. Our findings describe a species-specific molecular panel for analysis of snow leopard scats, and highlight the efficacy of noninvasive genetic surveys for monitoring snow leopards. These methods enable large-scale noninvasive studies that will provide information critical for conservation of snow leopards.
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Janecka, J. E., Jackson, R., Munkhtsog, B., Murphy, W. J. (2014). Characterization of 9 microsatellites and primers in snow leopards and a species-specific PCR assay for identifying noninvasive samples. Conservation Genetic Resource, 6(2), 369:373.
Abstract: Molecular markers that can effectively identify noninvasively collected samples and provide genetic
information are critical for understanding the distribution, status, and ecology of snow leopards (Panthera uncia). However, the low DNA quantity and quality in many
noninvasive samples such as scats makes PCR amplification and genotyping challenging. We therefore designed primers for 9 microsatellites loci previously isolated in the
domestic cat (Felis catus) specifically for snow leopard studies using noninvasive samples. The loci showed moderate levels of variation in two Mongolian snow leopard
populations. Combined with seven other loci that we previously described, they have sufficient variation (He = 0.504, An = 3.6) for individual identification and
population structure analysis. We designed a species species specific PCR assay using cytochrome b for identification of unknown snow leopard samples. These molecular markers
facilitate in depth studies to assess distribution, abundance, population structure, and landscape connectivity of this endangered species.
endangered species
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Janecka, J. E., Jackson, R., Munkhtsog, B., Murphy, W. J. (2014). Characterization of 9 microsatellites and primers in snow leopards and a species-specific PCR assay for identifying noninvasive samples. Conservation Genetic Resource, 6(2), 369:373.
Abstract: Molecular markers that can effectively identify noninvasively collected samples and provide genetic
information are critical for understanding the distribution, status, and ecology of snow leopards (Panthera uncia). However, the low DNA quantity and quality in many
noninvasive samples such as scats makes PCR amplification and genotyping challenging. We therefore designed primers for 9 microsatellites loci previously isolated in the
domestic cat (Felis catus) specifically for snow leopard studies using noninvasive samples. The loci showed moderate levels of variation in two Mongolian snow leopard
populations. Combined with seven other loci that we previously described, they have sufficient variation (He = 0.504, An = 3.6) for individual identification and
population structure analysis. We designed a species species specific PCR assay using cytochrome b for identification of unknown snow leopard samples. These molecular markers
facilitate in depth studies to assess distribution, abundance, population structure, and landscape connectivity of this endangered species.
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Janecka, J. E., Alves, P., Karmacharya, D., Samsel, N., Cheng, E., Tallmom, D., Schwartz, M. (2013). Wildlife Genetics in Mountainous Rugged Asian Landscapes: Methods, Applications and Examples. In Wildlife Research Techniques in rugged Mountainous Asian Landscapes (pp. 44–91).
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Janeč, & ka, J. E., Munkhtsog, B., Jackson, R.M., Naranbaatar, G., Mallon, D.P. & Murphy, W.J. (2011). Comparison of noninvasive genetic and camera-trapping techniques for surveying snow leopards. Journal of Mammalogy, 92(4), 771–783.
Abstract: The endangered snow leopard (Panthera uncia) is widely but sparsely distributed throughout the mountainous regions of central Asia. Detailed information on the status and abundance of the snow leopard is limited because of the logistical challenges faced when working in the rugged terrain it occupies, along with its secretive nature. Camera-trapping and noninvasive genetic techniques have been used successfully to survey this felid. We compared noninvasive genetic and camera-trapping snow leopard surveys in the Gobi Desert of Mongolia. We collected 180 putative snow leopard scats from 3 sites during an 8-day period along 37.74 km of transects. We then conducted a 65-day photographic survey at 1 of these sites, approximately 2 months after scat collection. In the site where both techniques were used noninvasive genetics detected 5 individuals in only 2 days of fieldwork compared to 7 individuals observed in the 65-day camera-trapping session. Estimates of population size from noninvasive genetics ranged between 16 and 19 snow leopards in the 314.3-km2 area surveyed, yielding densities of 4.9–5.9 individuals/100 km2. In comparison, the population estimate from the 65-day photographic survey was 4 individuals (adults only) within the 264-km2 area, for a density estimate of 1.5 snow leopards/100 km2. Higher density estimates from the noninvasive genetic survey were due partly to an inability to determine age and exclude subadults, reduced spatial distribution of sampling points as a consequence of collecting scats along linear transects, and deposition of scats by multiple snow leopards on common sites. Resulting differences could inflate abundance estimated from noninvasive genetic surveys and prevent direct comparison of densities derived from the 2 approaches unless appropriate adjustments are made to the study design.
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Jamtsho, Y., Katel, O. (2019). Livestock depredation by snow leopard and Tibetan wolf: Implications for herders� livelihoods in Wangchuck Centennial National Park, Bhutan. Springer Open, (9:1), 1–10.
Abstract: Human-wildlife conflict (HWC) is a serious problem in many parts of the world, and Bhutan�s Wangchuck Centennial
National Park (WCNP) is no exception. Located in the remote alpine areas of the eastern Himalaya, wildlife species
such as snow leopard (SL) and Tibetan wolf (TW) are reported to kill livestock in many parts of the Park. Such
depredation is believed to have affected the livelihoods of high-altitude herding communities, resulting in conflicts
between them. This study provides analysis on the extent of livestock depredation by wildlife predators such as SL
and TW and examines its implications for the livelihoods of herding communities of Choekhortoe and Dhur regions
of WCNP. Using semi-structured questionnaires, all herders (n = 38) in the study area were interviewed. The questions
pertained to livestock population, frequency of depredation and income lost due to depredation in the last five years
from 2012 to 2016. This study recorded 2,815 livestock heads in the study area, with an average herd size of 74.1 stock.
The average herd size holding showed a decreasing trend over the years, and one of the reasons cited by the herders
is depredation by SL and TW and other predators. This loss equated to an average annual financial loss equivalent to
10.2% (US$837) of their total per capita cash income. Such losses have resulted in negative impacts on herders�
livelihood; e.g. six herders (2012-2016) even stopped rearing livestock and resorted to an alternate source of cash
income. The livestock intensification programmes, including pasture improvement through allowing controlled
burning, and financial compensation, may be some potential short-term solutions to reduce conflict between herders
and predators. Issuing permits for cordyceps (Ophiocordyceps sinensis) collection only to the herders and instilling the
sense of stewardship to highland herders may be one of the long-term solutions.
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Jalanka, H. H., & Roeken, B. (1990). The use of Medetomidine, Medetomidine-Ketamine combinations, and Atipamezole in nondomestic mammals: A review. Journal-of-Zoo-and-Wildlife-Medicine, 21(3), 259–282.
Abstract: The recent development of potent and specifica lphar-adrenoceptoar gonistsa nd antagonists has enhanced their use in nondomestic animal immobilization and reversal. Medetomidine, a new potent alphar-agonist, in combination with the dissociative anesthetic ketamine, has been used to immobilize a variety of nondomestic mammals. Medetomidine alone induces sedation in a dose-dependent way, and complete immobilization has been achieved with high doses in semidomesticated reindeer (Rangifer tarandus) and blue foxes (Alopex lagopus). Howbver, we feel that ketamine should be added to the immobilization mixture to ensure complete immobilization and operator safety. In ketamine combinations, medetomidine doses are usually 60-100 pg/kg. The required ketamine doses are remarkably low:0.8-1.6 mglkg in most ruminants,2.5-3.0 mgUgin felids,u rsids,a nd canids,a nd 5.G-8.0m glkgi n primates,w olverines(Gulog ulo),ando therm uitelids. Clinically, the resulting immobilization is characterized by a smooth onset, good to excellent myorelaxation, and areflexia at higher doses. Determinations of hematologic, serum biochemicil, arterial blood gas,a nd acid-bases tatusp arametersi ndicate that the immobilization is physiologically sound. We have had no fatalities attributable to the immobilization mixture ( I ,240 immobilizations). The alphar-adrenoceptora ntagonist,a tipamezole,i s highly efective in reversingt he immobilization induced by medetomidine, medetomidine-ketamine combinations, or xylazine. In ruminants, the medetomidine-ketamine-induced immobilization can be rapidly and persistently reversed by administering 100-l 50 1rg/kg of alipamezole i.v. and the rest s.c., adjusting the total atipamezole dose to an atipamezole: medetomidine ratio of approximately 4-5 (w/w). Becauseth e required ketamine doses are relatively high in carnivores, we prefer to use a lower atipamezole dose (totil atipamezoie: medetomidine ratio approximately 2-3 w/w) and to administer it i.m. or s.c. Using thii regimen, reversals are calm and animals show minimal “residual ketamine effect.” Because atipamezole is a competitive antagonist, its dose should be reduced if it is administered late in the immobilization period when a large part of medetomidine has been endogenously metabolized. Xylazine-induced immobilization is rapidly reversed by I mg of atipamezole for every 8-12 mg of xylazine used.
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Jalanka, H. H. (1989). Medetomidine-induced and ketamine-induced immobilization of snow leopards (Panthera uncia) doses, evaluation and reversal by atipamezole. Journal of Zoo and Wildlife Medicine, 20(2), 154–162.
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Jalanka, H. H. (1989). Evaluation and comparison of 2 ketamine-based immobilization techniques in snow leopards (Panthera uncia). Journal of Zoo and Wildlife Medicine, 20(2), 163–169.
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